Move AugurError to new errors.py, replace RuntimeError

[victorlin]

Description of proposed changes

See commit messages.

Related issue(s)

Suggested by @tsibley: #918 (review)

Testing

Tests modified accordingly.

[victorlin]

Cyclic dependency between augur.utils and augur.util_support...

[codecov]

Codecov Report

Merging #921 (2ad9b2b) into master (5916362) will increase coverage by 0.02%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #921      +/-   ##
==========================================
+ Coverage   59.34%   59.36%   +0.02%     
==========================================
  Files          42       43       +1     
  Lines        6011     6014       +3     
  Branches     1539     1539              
==========================================
+ Hits         3567     3570       +3     
  Misses       2185     2185              
  Partials      259      259              

Impacted Files	Coverage Δ
augur/utils.py	64.34% <ø> (-0.31%)	⬇️
augur/__init__.py	79.36% <100.00%> (+0.33%)	⬆️
augur/errors.py	100.00% <100.00%> (ø)
augur/filter.py	96.24% <100.00%> (+<0.01%)	⬆️
augur/parse.py	89.02% <100.00%> (ø)
augur/util_support/node_data_file.py	100.00% <100.00%> (ø)

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[huddlej]

Thanks, @victorlin! What if we placed AugurError in a new errors.py or exceptions.py top-level module in augur (sort of like pandas does, only simpler)? This organization should address this and future circular import issues. I also prefer from .errors import AugurError over from .utils import AugurError for readability.

[victorlin]

@huddlej good suggestion, done: 2af1045

[victorlin]

Would you rather keep or drop 7a72c25? I'm fine with either.

[huddlej]

@victorlin I'd probably drop that change for now. Seeing all of those imports at the top should be a good reminder for us to move the util support logic back into utils at some point... :)

[tsibley]

LGTM by inspection. Using a separate "errors" module is also what I'd done for nextstrain.cli.errors, as exception classes are used/imported so widely it's good not to have them wrapped up with other stuff.